final JInternalFrame frame;\r
JScrollPane scrollPane = new JScrollPane();\r
JTable table;\r
+ JPanel groupPanel;\r
+\r
+ boolean alignmentHasFeatures = false;\r
\r
public FeatureSettings(AlignViewport av, final AlignmentPanel ap)\r
{\r
frame = new JInternalFrame();\r
frame.setContentPane(this);\r
Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 300);\r
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
\r
setTableData();\r
\r
- final JSlider transparency = new JSlider(0, 70, 0);\r
+ final JSlider transparency = new JSlider(0, 70, 100 - (int)(fr.transparency*100) );\r
transparency.addChangeListener(new ChangeListener()\r
{\r
public void stateChanged(ChangeEvent evt)\r
JPanel transPanel = new JPanel(new FlowLayout());\r
transPanel.add(new JLabel("Transparency"));\r
transPanel.add(transparency);\r
+ JButton button = new JButton("Invert Selection");\r
+ transPanel.add(button);\r
+ button.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ invertSelection();\r
+ }\r
+ });\r
\r
//////////////////////////////////////////////\r
//We're going to need those OK cancel buttons\r
JPanel buttonPanel = new JPanel(new FlowLayout());\r
- JButton button = new JButton("OK");\r
+ button = new JButton("OK");\r
button.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent evt)\r
JPanel bigPanel = new JPanel(new BorderLayout());\r
bigPanel.add(transPanel, BorderLayout.SOUTH);\r
bigPanel.add(scrollPane, BorderLayout.CENTER);\r
+ if(groupPanel!=null)\r
+ {\r
+ groupPanel.setLayout(\r
+ new GridLayout(fr.featureGroups.size() / 4 + 1, 4));\r
\r
+ groupPanel.validate();\r
+ bigPanel.add(groupPanel, BorderLayout.NORTH);\r
+ }\r
add(bigPanel, BorderLayout.CENTER);\r
add(buttonPanel, BorderLayout.SOUTH);\r
\r
\r
void setTableData()\r
{\r
+ alignmentHasFeatures = false;\r
+\r
+ if (fr.featureGroups == null)\r
+ fr.featureGroups = new Hashtable();\r
+\r
Vector allFeatures = new Vector();\r
- Vector features;\r
- Enumeration e;\r
- SequenceFeature sf;\r
+ Vector allGroups = new Vector();\r
+ SequenceFeature[] tmpfeatures;\r
+ String group;\r
\r
- for(int i=0; i< av.alignment.getHeight(); i++)\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
- features = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
- if(features==null)\r
- continue;\r
+ if (av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)\r
+ continue;\r
+\r
+ alignmentHasFeatures = true;\r
+\r
+ tmpfeatures = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
+\r
+ int index = 0;\r
+ while (index < tmpfeatures.length)\r
+ {\r
+ if(tmpfeatures[index].begin == 0 && tmpfeatures[index].end ==0)\r
+ {\r
+ index++;\r
+ continue;\r
+ }\r
+\r
+ if(tmpfeatures[index].getFeatureGroup()!=null)\r
+ {\r
+ group = tmpfeatures[index].featureGroup;\r
+ if(!allGroups.contains(group))\r
+ {\r
+ allGroups.addElement(group);\r
+\r
+ boolean visible = true;\r
+ if (fr.featureGroups.containsKey(group))\r
+ {\r
+ visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();\r
+ }\r
+\r
+ fr.featureGroups.put(group, new Boolean(visible));\r
+\r
+ if (groupPanel == null)\r
+ {\r
+ groupPanel = new JPanel();\r
+ }\r
+\r
+ final JCheckBox check = new JCheckBox(group, visible);\r
+ check.setFont(new Font("Serif", Font.BOLD, 12));\r
+ check.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent evt)\r
+ {\r
+ fr.featureGroups.put(check.getText(),\r
+ new Boolean(check.isSelected()));\r
+ ap.seqPanel.seqCanvas.repaint();\r
+ if (ap.overviewPanel != null)\r
+ ap.overviewPanel.updateOverviewImage();\r
+\r
+ resetTable(true);\r
+ }\r
+ });\r
+ groupPanel.add(check);\r
+\r
+ }\r
+\r
+ }\r
\r
- e = features.elements();\r
- while(e.hasMoreElements())\r
+ if (!allFeatures.contains(tmpfeatures[index].getType()))\r
{\r
- sf = (SequenceFeature)e.nextElement();\r
- if(!allFeatures.contains(sf.getType()))\r
- {\r
- allFeatures.addElement(sf.getType());\r
- }\r
+ allFeatures.addElement(tmpfeatures[index].getType());\r
}\r
+ index ++;\r
}\r
- if(allFeatures.size()<1)\r
+ }\r
+\r
+\r
+ if(!alignmentHasFeatures)\r
{\r
- try{\r
- frame.setClosed(true);\r
- }catch(Exception ex){}\r
+ try\r
+ { frame.setClosed(true); }\r
+ catch (Exception ex){}\r
+\r
+ JOptionPane.showInternalMessageDialog(\r
+ Desktop.desktop, "No features have been added to this alignment!",\r
+ "No Sequence Features", JOptionPane.WARNING_MESSAGE);\r
+\r
return;\r
}\r
\r
- int fSize = allFeatures.size();\r
+ resetTable(false);\r
+ }\r
+\r
+ void resetTable(boolean groupsChanged)\r
+ {\r
+ SequenceFeature [] tmpfeatures;\r
+ String group=null, type;\r
+ Vector visibleChecks = new Vector();\r
+\r
+ //Find out which features should be visible depending on which groups\r
+ //are selected / deselected\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ {\r
+ if (av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)\r
+ continue;\r
\r
- String type;\r
- boolean originalExists = false;\r
- if(originalData!=null)\r
- originalExists = true;\r
- else\r
- originalData = new Object[fSize][3];\r
+ tmpfeatures = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
+ int index = 0;\r
+ while (index < tmpfeatures.length)\r
+ {\r
+ group = tmpfeatures[index].featureGroup;\r
+\r
+ if(tmpfeatures[index].begin==0 && tmpfeatures[index].end==0)\r
+ {\r
+ index ++;\r
+ continue;\r
+ }\r
+\r
+ if (group==null || fr.featureGroups.get(group)==null ||\r
+ ((Boolean) fr.featureGroups.get(group)).booleanValue())\r
+ {\r
+ type = tmpfeatures[index].getType();\r
+ if(!visibleChecks.contains(type) )\r
+ {\r
+ visibleChecks.addElement(type);\r
+ }\r
+ }\r
+ index++;\r
+ }\r
+ }\r
\r
+ int fSize = visibleChecks.size();\r
Object [][] data = new Object[fSize][3];\r
- for(int i=0; i<fSize; i++)\r
+ int dataIndex = 0;\r
+\r
+ if(fr.renderOrder!=null)\r
{\r
- type = allFeatures.elementAt(i).toString();\r
- Color col = fr.getColour(type);\r
- data[i][0]=type;\r
- data[i][1]=col;\r
- if(fr.featuresDisplayed!=null)\r
- data[i][2] = new Boolean(fr.featuresDisplayed.contains(type));\r
- else\r
- data[i][2] = new Boolean(true);\r
-\r
- if(!originalExists)\r
+ //First add the checks in the previous render order,\r
+ //in case the window has been closed and reopened\r
+ for(int ro=fr.renderOrder.length-1; ro>-1; ro--)\r
{\r
- originalData[i][0] = type;\r
- originalData[i][1] = col;\r
- if (fr.featuresDisplayed != null)\r
- originalData[i][2] = new Boolean(fr.featuresDisplayed.contains(type));\r
- else\r
- originalData[i][2] = new Boolean(true);\r
+ type = fr.renderOrder[ro];\r
+\r
+ if(!visibleChecks.contains(type))\r
+ continue;\r
+\r
+ data[dataIndex][0] = type;\r
+ data[dataIndex][1] = fr.getColour(type);\r
+ data[dataIndex][2] = new Boolean(av.featuresDisplayed.containsKey(type));\r
+ dataIndex++;\r
+ visibleChecks.removeElement(type);\r
}\r
}\r
- ////////////////////////////////////\r
- //Now build the table\r
- table = new JTable(new FeatureTableModel(data));\r
- scrollPane.setViewportView(table);\r
- table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));\r
- table.setFont(new Font("Verdana", Font.PLAIN, 12));\r
- table.setDefaultRenderer(Color.class,\r
- new ColorRenderer());\r
\r
- table.setDefaultEditor(Color.class,\r
- new ColorEditor());\r
+ fSize = visibleChecks.size();\r
+ for(int i=0; i<fSize; i++)\r
+ {\r
+ //These must be extra features belonging to the group\r
+ //which was just selected\r
+ type = visibleChecks.elementAt(i).toString();\r
+ data[dataIndex][0] = type;\r
\r
- table.getColumnModel().getColumn(0).setPreferredWidth(200);\r
+ if(fr.getColour(type)==null)\r
+ fr.createRandomColour(type);\r
\r
- table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
+ data[dataIndex][1] = fr.getColour(type);\r
+ data[dataIndex][2] = new Boolean(true);\r
+ dataIndex++;\r
+ }\r
\r
- table.addMouseListener(new MouseAdapter()\r
- {\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- selectedRow = table.rowAtPoint(evt.getPoint());\r
- }\r
- });\r
+ if(originalData==null)\r
+ {\r
+ originalData = new Object[data.length][3];\r
+ System.arraycopy(data,0,originalData,0,data.length);\r
+ }\r
\r
- table.addMouseMotionListener(new MouseMotionAdapter()\r
- {\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- int newRow = table.rowAtPoint(evt.getPoint());\r
- if(newRow!=selectedRow\r
- && selectedRow!=-1\r
- && newRow!=-1)\r
- {\r
- Object[] temp = new Object[3];\r
- temp[0] = table.getValueAt(selectedRow, 0);\r
- temp[1] = table.getValueAt(selectedRow, 1);\r
- temp[2] = table.getValueAt(selectedRow, 2);\r
-\r
- table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);\r
- table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);\r
- table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);\r
-\r
- table.setValueAt(temp[0], newRow, 0);\r
- table.setValueAt(temp[1], newRow, 1);\r
- table.setValueAt(temp[2], newRow, 2);\r
-\r
- selectedRow = newRow;\r
- }\r
- }\r
+ table = new JTable(new FeatureTableModel(data));\r
+ scrollPane.setViewportView(table);\r
+ table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));\r
+ table.setFont(new Font("Verdana", Font.PLAIN, 12));\r
+ table.setDefaultRenderer(Color.class,\r
+ new ColorRenderer());\r
+\r
+ table.setDefaultEditor(Color.class,\r
+ new ColorEditor());\r
+\r
+ table.getColumnModel().getColumn(0).setPreferredWidth(200);\r
+\r
+ table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
+\r
+ table.addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ selectedRow = table.rowAtPoint(evt.getPoint());\r
+ }\r
});\r
\r
+ table.addMouseMotionListener(new MouseMotionAdapter()\r
+ {\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ int newRow = table.rowAtPoint(evt.getPoint());\r
+ if(newRow!=selectedRow\r
+ && selectedRow!=-1\r
+ && newRow!=-1)\r
+ {\r
+ Object[] temp = new Object[3];\r
+ temp[0] = table.getValueAt(selectedRow, 0);\r
+ temp[1] = table.getValueAt(selectedRow, 1);\r
+ temp[2] = table.getValueAt(selectedRow, 2);\r
+\r
+ table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);\r
+ table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);\r
+ table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);\r
+\r
+ table.setValueAt(temp[0], newRow, 0);\r
+ table.setValueAt(temp[1], newRow, 1);\r
+ table.setValueAt(temp[2], newRow, 2);\r
+\r
+ selectedRow = newRow;\r
+ }\r
+ }\r
+ });\r
+\r
+ updateFeatureRenderer(data);\r
+\r
}\r
\r
void load()\r
Enumeration e = fr.featureColours.keys();\r
while(e.hasMoreElements())\r
{\r
-\r
-\r
jalview.binding.Colour col = new jalview.binding.Colour();\r
col.setName(e.nextElement().toString());\r
col.setRGB(jalview.util.Format.getHexString(\r
ex.printStackTrace();\r
}\r
}\r
+ }\r
+\r
+ public void invertSelection()\r
+ {\r
+ for(int i=0; i<table.getRowCount(); i++)\r
+ {\r
+ Boolean value = (Boolean)table.getValueAt(i,2);\r
+\r
+ table.setValueAt(\r
+ new Boolean(!value.booleanValue()),\r
+ i,2);\r
+ }\r
\r
}\r
\r
{\r
fr.setFeaturePriority( data );\r
ap.repaint();\r
+\r
+ if(ap.overviewPanel!=null)\r
+ ap.overviewPanel.updateOverviewImage();\r
}\r
\r
int selectedRow =-1;\r
return data;\r
}\r
\r
+ public void setData(Object[][] data)\r
+ {\r
+ this.data = data;\r
+ }\r
+\r
public int getColumnCount() {\r
return columnNames.length;\r
}\r
git://source.jalview.org / jalview.git / blobdiff